[Chimera-users] Potential Energy Calculations
Nikolay Igorovich Rodionov
nirodion at syr.edu
Fri Sep 21 17:49:00 PDT 2012
Okay will do, thanks for the advice!
Nikolay Rodionov| MBA Candidate & B.S. Bioengineering 2015
Martin J. Whitman School of Management & L.C. Smith College of Engineering
at Syracuse University
Syracuse, New York 13244
Phone: 281.301.9401| Email: Nirodion at syr.edu
On 9/21/12 8:41 PM, "Elaine Meng" <meng at cgl.ucsf.edu> wrote:
>In my opinion, no. Maybe you could ask for recommendations of what
>program(s) would be more appropriate on ccl.net -- we're getting into the
>territory of general computational chemistry issues that are probably
>beyond the scope of this forum.
>On Sep 21, 2012, at 5:30 PM, Nikolay Igorovich Rodionov wrote:
>> Would it be make sense to compute the total energy for the protein w/o
>> water and then loaded with water, and then take the difference to be
>> energy due to interaction?
>> Nikolay Rodionov| MBA Candidate & B.S. Bioengineering 2015
>> Martin J. Whitman School of Management & L.C. Smith College of
>> at Syracuse University
>> Syracuse, New York 13244
>> Phone: 281.301.9401| Email: Nirodion at syr.edu
>> On 9/21/12 8:23 PM, "Elaine Meng" <meng at cgl.ucsf.edu> wrote:
>>> Hi Nikolay,
>>> Sorry, no. Although the minimizer reports an energy, it is the total
>>> energy of the system, and no breakdown is available.
>>> Elaine C. Meng, Ph.D.
>>> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
>>> Department of Pharmaceutical Chemistry
>>> University of California, San Francisco
>>> On Sep 21, 2012, at 4:32 PM, Nikolay Igorovich Rodionov wrote:
>>>> Hi all,
>>>> I was wondering the there is a tool in chimera that can find the net
>>>> interaction potential energy between models, something like Lennard
>>>> Jones Potential. Specifically, I need to measure the interaction
>>>> potential between a protein and water in a solvated system.
>>>> Nikolay Rodionov
>> Chimera-users mailing list
>> Chimera-users at cgl.ucsf.edu
More information about the Chimera-users